Epidemiology of SARS-CoV-2 Omicron BA.5 Infections, Macau, June–July 2022

A SARS-CoV-2 Omicron BA.5 outbreak occurred in Macau from mid-June through July 2022. Out of >1,800 laboratory-confirmed cases, most were mild or asymptomatic; only 6 deaths were recorded. The outbreak was controlled through stringent public health and social measures, such as repeated universal testing and a stay-at-home order lasting 2 weeks.


Model details
We estimated the time-varying reproductive number (Rt) from real data as previously described (2). In brief, the Rt assumes that the distribution of infectiousness through time is independent of calendar time. Transmission is then modeled by using a Poisson process. The probability distribution w(s) denotes the infectiousness profile since infection; therefore, the rate .
The true number of infection cases was unobserved because we only observed new local cases reported on day k [Y(k)]. To overcome this challenge, we used: where R(t) is the time-varying effective reproductive number at time t.

Likelihood function
We used the smoothing method as previously described (2), assuming that the transmissibility was constant over a time period [t − τ + 1, t], where τ is the smoothing parameter. Hence, likelihood of infection incidence during this time period was: . The total likelihood is the product of the individual likelihood at each time t in the observed data. The first τ − 1 days were excluded because of τday smoothing.

Prior Probability Distribution
We assumed the prior probability distribution for R(t) was a gamma distribution (parameters 1, 5) (mean 5, SD +5).

Estimate of Model Parameters
We conducted our analysis in a Bayesian framework and used the Markov chain Monte Carlo method (3) to estimate model parameters. At each step k, we updated the model parameters θ by using the random walk Metropolis-Hastings algorithm (3). The step size of the proposal was adjusted to have an acceptance rate of 20%-30%.

Assumptions for Input Parameters
For incubation period distribution, we use the estimated distribution mean of 3.2 days.
The empirical distribution of delay from disease onset to report was set as follows: 50% probability delayed by day 1, 40% by day 2, and 8% by day 3, then the remaining 2% probability was equally distributed over days 4-20. According to those distributions, we constructed the distribution for delay from initial infection to report by convoluting the incubation period distribution and empirical distribution of delay from onset to report. We then used a deconvolution approach (4) to obtain the epidemic curve by infection time, which was achieved by using the fit incidence function in the incidental package in R (The R Project for Statistical Computing, https://www.r-project.org).
The infectiousness since infection w t was a convolution of incubation period and infectiousness relative to onset (allowed to be presymptomatic) according to viral shedding data with a shifted gamma distribution (mean 12.3 days, SD +8 days) (5); therefore, the shift parameter c was 12.3 days. Peak infectiousness was on day 0. We proposed an infectiousness profile gc(t1 − ts1) that described the probability of a transmission event occurring at time t1 after illness onset ts1. We assumed a gamma distribution g(t) with a time shift to determine the start of infectiousness c days before symptom onset; therefore, gc(t) = g(t + c) determined presymptomatic transmission. We analyzed the epidemic curve until July 31, 2022, and used τ = 7 in our analysis to avoid unstable estimates for time-varying reproductive numbers. Quarantine Zone-specific, multi-level focused approach to epidemic prevention and control activated. Closure and control measures implemented for living areas of persons with confirmed cases. Nucleic acid tests will temporarily be conducted on days 1-3, 5, and 7. Only entry into but no exit from the zone will be permitted with the exception of staff for red-coded zones. No person can leave the zone until the first test is concluded for yellow-coded zones. Date announced Source same day before they could be converted back to a green code. If the RAT was not done for 2 consecutive days, the code would be changed to red, and NAT would be required. The code could be changed back to green after a negative NAT. 2022 Jul 4 Clinical Citywide NAT Launch of citywide NAT from 9:00 AM July 4 to 6:00 PM on July 9. The 4th round of NAT was July 4-5, 5th round was July 6-7, and 6th round was July 8-9.
2022 Jul 3 https://www.gcs.gov.mo/det ail/en/N22GCad4aM?9 2022 Jul 9 Community Relatively static management Macao suspended all non-essential industrial and commercial activities from 0:00 AM on July 11 to 0:00 AM on July 18 and called on residents to minimize movement to reduce risk of virus transmission, except for those persons whose activity was deemed essential to the community and day-to-day lives of the public.